Comparison of salamander eye size with other vertebrate groups
Katie Thomas & Nicole Bednarik
2022-12-21
Import data and phylogenies
Frogs
## [1] TRUE
Salamanders
Fishes
## [1] TRUE
Squamates
## [1] FALSE
Cornea diameter vs. mass
Frogs
Match data to tree & fit PGLS in caper
## $tree_not_data
## [1] "Anodonthyla_boulengerii_Microhylidae"
## [2] "Leptobrachella_bidoupensis_Megophryidae"
## [3] "Microhyla_fissipes_Microhylidae"
## [4] "Microhyla_fusca_Microhylidae"
## [5] "Microhyla_marmorata_Microhylidae"
## [6] "Microhyla_pulverata_Microhylidae"
## [7] "Nasikabatrachus_sahyadrensis_Nasikabatrachidae"
##
## $data_not_tree
## character(0)## [1] "Leptobrachella_bidoupensis_Megophryidae"
## [2] "Nasikabatrachus_sahyadrensis_Nasikabatrachidae"
## [3] "Anodonthyla_boulengerii_Microhylidae"
## [4] "Microhyla_pulverata_Microhylidae"
## [5] "Microhyla_fusca_Microhylidae"
## [6] "Microhyla_fissipes_Microhylidae"
## [7] "Microhyla_marmorata_Microhylidae"## character(0)
##
## Call:
## pgls(formula = log10(cor_av) ~ log10(mass_av), data = frog.cdmass.comp,
## lambda = "ML", param.CI = 0.95)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.28753 -0.06242 -0.01143 0.04899 0.39358
##
## Branch length transformations:
##
## kappa [Fix] : 1.000
## lambda [ ML] : 0.875
## lower bound : 0.000, p = < 2.22e-16
## upper bound : 1.000, p = 3.1392e-08
## 95.0% CI : (0.775, 0.940)
## delta [Fix] : 1.000
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.368374 0.055494 6.6381 2.639e-10 ***
## log10(mass_av) 0.747702 0.031120 24.0266 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.09844 on 211 degrees of freedom
## Multiple R-squared: 0.7323, Adjusted R-squared: 0.7311
## F-statistic: 577.3 on 1 and 211 DF, p-value: < 2.2e-16Salamanders
Match data to tree & fit PGLS in caper
## $tree_not_data
## character(0)
##
## $data_not_tree
## [1] "Pleurodeles_waltl_gilled"## character(0)## [1] "Pleurodeles_waltl_gilled"
##
## Call:
## pgls(formula = log10(cor_av) ~ log10(rootmass_av), data = sal.cdmass.comp,
## lambda = "ML", param.CI = 0.95)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.031038 -0.005368 -0.000095 0.004781 0.041013
##
## Branch length transformations:
##
## kappa [Fix] : 1.000
## lambda [ ML] : 0.832
## lower bound : 0.000, p = 8.4377e-15
## upper bound : 1.000, p = 5.6595e-09
## 95.0% CI : (0.683, 0.922)
## delta [Fix] : 1.000
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.184679 0.057335 3.2211 0.001566 **
## log10(rootmass_av) 0.586098 0.051971 11.2773 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.01006 on 150 degrees of freedom
## Multiple R-squared: 0.4588, Adjusted R-squared: 0.4552
## F-statistic: 127.2 on 1 and 150 DF, p-value: < 2.2e-16Plot for cornea vs. mass
Plot that includes color codes for habitat in addition to regressions for frogs & salamanders
Add traits to frog and salamander datasets
Stopping here because want to discuss before proceeding further.
Eye diameter vs. mass
Frogs
Match data to tree & fit PGLS in caper
## $tree_not_data
## [1] "Leptobrachella_bidoupensis_Megophryidae"
## [2] "Microhyla_fissipes_Microhylidae"
## [3] "Microhyla_fusca_Microhylidae"
## [4] "Microhyla_marmorata_Microhylidae"
## [5] "Microhyla_pulverata_Microhylidae"
##
## $data_not_tree
## character(0)## [1] "Leptobrachella_bidoupensis_Megophryidae"
## [2] "Microhyla_pulverata_Microhylidae"
## [3] "Microhyla_fusca_Microhylidae"
## [4] "Microhyla_fissipes_Microhylidae"
## [5] "Microhyla_marmorata_Microhylidae"## character(0)
##
## Call:
## pgls(formula = log10(eye_av) ~ log10(mass_av), data = frog.edmass.comp,
## lambda = "ML", param.CI = 0.95)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.39281 -0.07739 -0.00560 0.06081 0.40551
##
## Branch length transformations:
##
## kappa [Fix] : 1.000
## lambda [ ML] : 0.961
## lower bound : 0.000, p = < 2.22e-16
## upper bound : 1.000, p = 0.012383
## 95.0% CI : (0.900, 0.994)
## delta [Fix] : 1.000
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.455710 0.062496 7.2918 5.916e-12 ***
## log10(mass_av) 0.822677 0.028023 29.3573 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.1084 on 213 degrees of freedom
## Multiple R-squared: 0.8018, Adjusted R-squared: 0.8009
## F-statistic: 861.9 on 1 and 213 DF, p-value: < 2.2e-16Salamanders
##
## Call:
## pgls(formula = log10(eye_av) ~ log10(rootmass_av), data = sal.cdmass.comp,
## lambda = "ML", param.CI = 0.95)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.0180704 -0.0036954 -0.0000669 0.0035026 0.0228160
##
## Branch length transformations:
##
## kappa [Fix] : 1.000
## lambda [ ML] : 0.845
## lower bound : 0.000, p = 3.0531e-11
## upper bound : 1.000, p = 2.8592e-06
## 95.0% CI : (0.658, 0.942)
## delta [Fix] : 1.000
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.398691 0.042603 9.3584 2.22e-16 ***
## log10(rootmass_av) 0.773017 0.041458 18.6458 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.006815 on 136 degrees of freedom
## (14 observations deleted due to missingness)
## Multiple R-squared: 0.7188, Adjusted R-squared: 0.7167
## F-statistic: 347.7 on 1 and 136 DF, p-value: < 2.2e-16Fishes
Match data to tree & fit PGLS in caper
## [1] "OK"## character(0)## character(0)
##
## Call:
## pgls(formula = log10(TD_av) ~ log10(mass_av), data = fishes.comp,
## lambda = "ML", param.CI = 0.95)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.051652 -0.008660 -0.000058 0.008999 0.061939
##
## Branch length transformations:
##
## kappa [Fix] : 1.000
## lambda [ ML] : 0.984
## lower bound : 0.000, p = < 2.22e-16
## upper bound : 1.000, p = 0.00017103
## 95.0% CI : (0.964, 0.996)
## delta [Fix] : 1.000
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.423092 0.195990 2.1587 0.03148 *
## log10(mass_av) 0.742976 0.031432 23.6379 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.01431 on 388 degrees of freedom
## (46 observations deleted due to missingness)
## Multiple R-squared: 0.5902, Adjusted R-squared: 0.5891
## F-statistic: 558.7 on 1 and 388 DF, p-value: < 2.2e-16Plot for eye vs. mass
Note that the salamander eye size dataset is msising the species with the smallest eyes (those had cornea measurements only), so that pushes the regression line up quite a bit.
Eye diameter vs. SVL
Frogs
Match data to tree & fit PGLS in caper
## [1] "OK"## character(0)## character(0)
##
## Call:
## pgls(formula = log10(eye_av) ~ log10(svl_av), data = frog.edsvl.comp,
## lambda = "ML", param.CI = 0.95)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.34569 -0.05473 0.00599 0.06458 0.31770
##
## Branch length transformations:
##
## kappa [Fix] : 1.000
## lambda [ ML] : 0.963
## lower bound : 0.000, p = < 2.22e-16
## upper bound : 1.000, p = 0.022769
## 95.0% CI : (0.902, 0.996)
## delta [Fix] : 1.000
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.664341 0.068331 -9.7224 < 2.2e-16 ***
## log10(svl_av) 0.837692 0.024418 34.3065 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.09626 on 218 degrees of freedom
## Multiple R-squared: 0.8437, Adjusted R-squared: 0.843
## F-statistic: 1177 on 1 and 218 DF, p-value: < 2.2e-16Salamanders
##
## Call:
## pgls(formula = log10(eye_av) ~ log10(svl_av), data = sal.cdmass.comp,
## lambda = "ML", param.CI = 0.95)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.0173372 -0.0021347 0.0006661 0.0041418 0.0154655
##
## Branch length transformations:
##
## kappa [Fix] : 1.000
## lambda [ ML] : 0.749
## lower bound : 0.000, p = 3.9968e-14
## upper bound : 1.000, p = 1.1559e-08
## 95.0% CI : (0.506, 0.898)
## delta [Fix] : 1.000
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.839890 0.079508 -10.564 < 2.2e-16 ***
## log10(svl_av) 0.782916 0.039652 19.745 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.005834 on 136 degrees of freedom
## (14 observations deleted due to missingness)
## Multiple R-squared: 0.7414, Adjusted R-squared: 0.7395
## F-statistic: 389.9 on 1 and 136 DF, p-value: < 2.2e-16Squamates
## $tree_not_data
## [1] "Acanthodactylus_boskianus" "Acanthodactylus_cantoris"
## [3] "Acanthodactylus_longipes" "Acanthodactylus_pardalis"
## [5] "Aeluroscalabotes_felinus" "Agkistrodon_piscivorus"
## [7] "Amblyrhynchus_cristatus" "Ameiva_ameiva"
## [9] "Anolis_trinitatis" "Basiliscus_basiliscus"
## [11] "Basiliscus_vittatus" "Bellatorias_frerei"
## [13] "Boa_constrictor" "Broadleysaurus_major"
## [15] "Brookesia_superciliaris" "Callisaurus_draconoides"
## [17] "Calotes_mystaceus" "Calotes_versicolor"
## [19] "Chalcides_ocellatus" "Chamaeleo_africanus"
## [21] "Chamaeleo_chamaeleon" "Chamaesaura_macrolepis"
## [23] "Coleonyx_elegans" "Coleonyx_variegatus"
## [25] "Cordylus_cordylus" "Cordylus_niger"
## [27] "Crotaphytus_bicinctores" "Crotaphytus_collaris"
## [29] "Ctenosaura_hemilopha" "Ctenosaura_similis"
## [31] "Cyrtodactylus_louisiadensis" "Dipsosaurus_dorsalis"
## [33] "Dracaena_guianensis" "Draco_melanopogon"
## [35] "Eremias_persica" "Eublepharis_hardwickii"
## [37] "Eublepharis_macularius" "Eugongylus_rufescens"
## [39] "Eumeces_schneideri" "Furcifer_lateralis"
## [41] "Furcifer_verrucosus" "Gallotia_atlantica"
## [43] "Gallotia_galloti" "Gekko_swinhonis"
## [45] "Gerrhosaurus_nigrolineatus" "Glaphyromorphus_nigricaudis"
## [47] "Gonatodes_ocellatus" "Gonocephalus_grandis"
## [49] "Heliobolus_lugubris" "Heloderma_suspectum"
## [51] "Hemidactylus_platycephalus" "Iguana_iguana"
## [53] "Karusasaurus_polyzonus" "Lacerta_agilis"
## [55] "Lacerta_viridis" "Leiocephalus_carinatus"
## [57] "Leiolepis_belliana" "Lepidodactylus_lugubris"
## [59] "Lepidophyma_gaigeae" "Liopholis_whitii"
## [61] "Lophognathus_longirostris" "Lygodactylus_picturatus"
## [63] "Meroles_anchietae" "Meroles_knoxii"
## [65] "Meroles_squamulosa" "Mesalina_guttulata"
## [67] "Narudasia_festiva" "Natrix_natrix"
## [69] "Phelsuma_astriata" "Phelsuma_madagascariensis"
## [71] "Phrynosoma_blainvillii" "Phrynosoma_cornutum"
## [73] "Phyllodactylus_reissii" "Platysaurus_guttatus"
## [75] "Platysaurus_intermedius" "Plestiodon_skiltonianus"
## [77] "Podarcis_muralis" "Pristurus_carteri"
## [79] "Pseudopus_apodus" "Python_molurus"
## [81] "Quedenfeldtia_moerens" "Saara_hardwickii"
## [83] "Sauromalus_ater" "Sceloporus_grammicus"
## [85] "Sceloporus_horridus" "Sceloporus_jarrovii"
## [87] "Sceloporus_magister" "Sceloporus_occidentalis"
## [89] "Scincus_mitranus" "Scincus_scincus"
## [91] "Sphaerodactylus_copei" "Sphenodon_punctatus"
## [93] "Takydromus_septentrionalis" "Tarentola_mauritanica"
## [95] "Thamnophis_melanogaster" "Thamnophis_sirtalis"
## [97] "Tiliqua_gigas" "Timon_lepidus"
## [99] "Trachylepis_perrotetii" "Trioceros_bitaeniatus"
## [101] "Trioceros_hoehnelii" "Tropidurus_hispidus"
## [103] "Tupinambis_teguixin" "Uma_exsul"
## [105] "Uranoscodon_superciliosus" "Uromastyx_aegyptia"
## [107] "Varanus_indicus" "Varanus_salvator"
## [109] "Xantusia_henshawi" "Xantusia_riversiana"
## [111] "Xantusia_vigilis"
##
## $data_not_tree
## character(0)## [1] "Sphenodon_punctatus" "Eremias_persica"
## [3] "Mesalina_guttulata" "Acanthodactylus_pardalis"
## [5] "Acanthodactylus_longipes" "Acanthodactylus_boskianus"
## [7] "Acanthodactylus_cantoris" "Heliobolus_lugubris"
## [9] "Meroles_anchietae" "Meroles_squamulosa"
## [11] "Meroles_knoxii" "Podarcis_muralis"
## [13] "Takydromus_septentrionalis" "Timon_lepidus"
## [15] "Lacerta_agilis" "Lacerta_viridis"
## [17] "Gallotia_galloti" "Gallotia_atlantica"
## [19] "Ameiva_ameiva" "Tupinambis_teguixin"
## [21] "Dracaena_guianensis" "Brookesia_superciliaris"
## [23] "Trioceros_bitaeniatus" "Trioceros_hoehnelii"
## [25] "Chamaeleo_chamaeleon" "Chamaeleo_africanus"
## [27] "Furcifer_lateralis" "Furcifer_verrucosus"
## [29] "Leiolepis_belliana" "Lophognathus_longirostris"
## [31] "Draco_melanopogon" "Gonocephalus_grandis"
## [33] "Calotes_versicolor" "Calotes_mystaceus"
## [35] "Uromastyx_aegyptia" "Saara_hardwickii"
## [37] "Phrynosoma_blainvillii" "Phrynosoma_cornutum"
## [39] "Uma_exsul" "Callisaurus_draconoides"
## [41] "Sceloporus_magister" "Sceloporus_occidentalis"
## [43] "Sceloporus_horridus" "Sceloporus_jarrovii"
## [45] "Sceloporus_grammicus" "Anolis_trinitatis"
## [47] "Leiocephalus_carinatus" "Basiliscus_vittatus"
## [49] "Basiliscus_basiliscus" "Dipsosaurus_dorsalis"
## [51] "Sauromalus_ater" "Iguana_iguana"
## [53] "Amblyrhynchus_cristatus" "Ctenosaura_hemilopha"
## [55] "Ctenosaura_similis" "Uranoscodon_superciliosus"
## [57] "Tropidurus_hispidus" "Crotaphytus_bicinctores"
## [59] "Crotaphytus_collaris" "Pseudopus_apodus"
## [61] "Heloderma_suspectum" "Varanus_salvator"
## [63] "Varanus_indicus" "Boa_constrictor"
## [65] "Python_molurus" "Agkistrodon_piscivorus"
## [67] "Natrix_natrix" "Thamnophis_melanogaster"
## [69] "Thamnophis_sirtalis" "Platysaurus_guttatus"
## [71] "Platysaurus_intermedius" "Karusasaurus_polyzonus"
## [73] "Chamaesaura_macrolepis" "Cordylus_niger"
## [75] "Cordylus_cordylus" "Broadleysaurus_major"
## [77] "Gerrhosaurus_nigrolineatus" "Lepidophyma_gaigeae"
## [79] "Xantusia_riversiana" "Xantusia_vigilis"
## [81] "Xantusia_henshawi" "Glaphyromorphus_nigricaudis"
## [83] "Eugongylus_rufescens" "Trachylepis_perrotetii"
## [85] "Liopholis_whitii" "Bellatorias_frerei"
## [87] "Tiliqua_gigas" "Chalcides_ocellatus"
## [89] "Plestiodon_skiltonianus" "Eumeces_schneideri"
## [91] "Scincus_scincus" "Scincus_mitranus"
## [93] "Aeluroscalabotes_felinus" "Eublepharis_macularius"
## [95] "Eublepharis_hardwickii" "Coleonyx_elegans"
## [97] "Coleonyx_variegatus" "Pristurus_carteri"
## [99] "Quedenfeldtia_moerens" "Sphaerodactylus_copei"
## [101] "Gonatodes_ocellatus" "Narudasia_festiva"
## [103] "Lygodactylus_picturatus" "Phelsuma_astriata"
## [105] "Phelsuma_madagascariensis" "Lepidodactylus_lugubris"
## [107] "Gekko_swinhonis" "Cyrtodactylus_louisiadensis"
## [109] "Hemidactylus_platycephalus" "Tarentola_mauritanica"
## [111] "Phyllodactylus_reissii"## character(0)
##
## Call:
## pgls(formula = log10(TD_av) ~ log10(svl_av) * Subgroup, data = squam.edsvl.comp,
## lambda = "ML", param.CI = 0.95)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.053486 -0.009735 -0.002637 0.008329 0.055101
##
## Branch length transformations:
##
## kappa [Fix] : 1.000
## lambda [ ML] : 1.000
## lower bound : 0.000, p = 0.00023366
## upper bound : 1.000, p = 1
## 95.0% CI : (0.794, NA)
## delta [Fix] : 1.000
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1.883245 0.244792 -7.6933 3.988e-12 ***
## log10(svl_av) 0.858776 0.063681 13.4855 < 2.2e-16 ***
## Subgroupgeckos 0.735057 0.351075 2.0937 0.03834 *
## log10(svl_av):Subgroupgeckos 0.081401 0.125112 0.6506 0.51650
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.01669 on 123 degrees of freedom
## Multiple R-squared: 0.6778, Adjusted R-squared: 0.6699
## F-statistic: 86.23 on 3 and 123 DF, p-value: < 2.2e-16Plot for eye vs. SVL
Note that the salamander eye size dataset is missing the species with the smallest eyes (those had cornea measurements only), so that pushes the regression line up quite a bit.
Figure
We can put these plots together to make a paneled figure
## quartz_off_screen
## 2